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GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation
Zhang H, et al.
Nature Communications
August 2021
Authors and Affiliates
Hongyi Zhang 1, Xiaowei Zhan 2, Bo Li 3,4;
1 Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
2 Department of Population and Data Science, UT Southwestern Medical Center, Dallas, TX, USA.
3 Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA. bo.li@utsouthwestern.edu.
4 Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA. bo.li@utsouthwestern.edu.
Systemic inhibition of PTPN22 augments anticancer immunity
Ho WJ, et al.
JCI
August 2021
Authors and Affiliates
Won Jin Ho 1, Sarah Croessmann 2, Jianping Lin 3, Zaw H Phyo 1, Soren Charmsaz 1, Ludmila Danilova 1, Aditya A Mohan 1, Nicole E Gross 1, Fangluo Chen 1, Jiajun Dong 3, Devesh Aggarwal 3, Yunpeng Bai 3, Janey Wang 4, Jing He 4, James M Leatherman 1, Mark Yarchoan 1, Todd D Armstrong 1, Neeha Zaidi 1, Elana J Fertig 1, Joshua C Denny 4, Ben H Park 2, Zhong-Yin Zhang 3, Elizabeth M Jaffee 5;
1 Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, United States of America.
2 Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America.
3 Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, United States of America.
4 Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States of America.
5 Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, United States of America.
Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers
Caushi JX, et al.
Nature
July 2021
Authors and Affiliates
Justina X Caushi #,1,2,3, Jiajia Zhang #,1,2,3, Zhicheng Ji 4,5, Ajay Vaghasia 3, Boyang Zhang 4, Emily Han-Chung Hsiue 3,6,7, Brian J Mog 3,6,7, Wenpin Hou 4, Sune Justesen 8, Richard Blosser 1,3, Ada Tam 1,3, Valsamo Anagnostou 1,3, Tricia R Cottrell 1,2,3,9, Haidan Guo 1,2,3, Hok Yee Chan 1,2,3, Dipika Singh 1,2,3, Sampriti Thapa 1,2,3, Arbor G Dykema 1,2,3, Poromendro Burman 1,2,3, Begum Choudhury 1,2,3, Luis Aparicio 1,2,3, Laurene S Cheung 1,2,3, Mara Lanis 1,3, Zineb Belcaid 1,3, Margueritta El Asmar 1,3, Peter B Illei 3, Rulin Wang 3, Jennifer Meyers 3, Kornel Schuebel 3, Anuj Gupta 3, Alyza Skaist 3, Sarah Wheelan 3, Jarushka Naidoo 1,3,10, Kristen A Marrone 1,3, Malcolm Brock 3, Jinny Ha 3, Errol L Bush 3, Bernard J Park 11, Matthew Bott 11, David R Jones 11, Joshua E Reuss 3,12, Victor E Velculescu 1,3, Jamie E Chaft 11, Kenneth W Kinzler 3,6,7, Shibin Zhou 3,6,7, Bert Vogelstein 3,6,7, Janis M Taube 1,2,3, Matthew D Hellmann 11, Julie R Brahmer 1,3, Taha Merghoub 11,13,14, Patrick M Forde 1,3, Srinivasan Yegnasubramanian 15,16,17, Hongkai Ji 18, Drew M Pardoll 19,20,21, Kellie N Smith 22,23,24;
1 Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA.
2 The Mark Center for Advanced Genomics and Imaging at Johns Hopkins, Baltimore, MD, USA.
3 Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA.
4 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
5 Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
6 Ludwig Center and Howard Hughes Medical Institute at Johns Hopkins, Baltimore, MD, USA.
7 Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
8 Immunitrack, Copenhagen, Denmark.
9 Ontario Institute for Cancer Research, Queens University, Kingston, Ontario, Canada.
10 Beaumont Hospital Dublin, RCSI University of Medicine and Health Science, Dublin, Ireland.
11 Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA.
12 Georgetown Lombardi Comprehensive Cancer Center at Georgetown University, Washington, DC, USA.
13 The Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
14 Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
15 Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA. syegnasu@jhmi.edu.
16 The Mark Center for Advanced Genomics and Imaging at Johns Hopkins, Baltimore, MD, USA. syegnasu@jhmi.edu.
17 Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA. syegnasu@jhmi.edu.
18 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. hji@jhu.edu.
19 Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA. dpardol1@jhmi.edu.
20 The Mark Center for Advanced Genomics and Imaging at Johns Hopkins, Baltimore, MD, USA. dpardol1@jhmi.edu.
21 Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA. dpardol1@jhmi.edu.
22 Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA. kellie@jhmi.edu.
23 The Mark Center for Advanced Genomics and Imaging at Johns Hopkins, Baltimore, MD, USA. kellie@jhmi.edu.
24 Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA. kellie@jhmi.edu.
# Contributed equally.
Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade
Andrews MC, et al.
Nature Medicine
July 2021
Authors and Affiliates
Miles C Andrews # 1 2 3, Connie P M Duong # 4 5 6, Vancheswaran Gopalakrishnan # 1, Valerio Iebba # 4 5, Wei-Shen Chen # 7 8, Lisa Derosa # 4 5 6, Md Abdul Wadud Khan 1, Alexandria P Cogdill 4 5 6 7, Michael G White 1, Matthew C Wong 7, Gladys Ferrere 4 5 6, Aurélie Fluckiger 4 5 6, Maria P Roberti 4 5 6, Paule Opolon 4, Maryam Tidjani Alou 4 5 6, Satoru Yonekura 4 5 6, Whijae Roh 7, Christine N Spencer 9, Irina Fernandez Curbelo 10, Luis Vence 10, Alexandre Reuben 11, Sarah Johnson 1, Reetakshi Arora 1, Golnaz Morad 1, Matthew Lastrapes 12, Erez N Baruch 7, Latasha Little 7, Curtis Gumbs 7, Zachary A Cooper 13, Peter A Prieto 14, Khalida Wani 15, Alexander J Lazar 7 15, Michael T Tetzlaff 15, Courtney W Hudgens 15, Margaret K Callahan 9 16, Matthew Adamow 16 17, Michael A Postow 16 17, Charlotte E Ariyan 18, Pierre-Olivier Gaudreau 1, Luigi Nezi 19, Didier Raoult 20, Catalin Mihalcioiu 21, Arielle Elkrief 22, Rossanna C Pezo 23, Lauren E Haydu 1, Julie M Simon 1, Hussein A Tawbi 24, Jennifer McQuade 24, Patrick Hwu 24, Wen-Jen Hwu 24, Rodabe N Amaria 24, Elizabeth M Burton 1, Scott E Woodman 7 24, Stephanie Watowich 10, Adi Diab 24, Sapna P Patel 24, Isabella C Glitza 24, Michael K Wong 24, Li Zhao 7, Jianhua Zhang 7, Nadim J Ajami 7, Joseph Petrosino 25, Robert R Jenq 7, Michael A Davies 24, Jeffrey E Gershenwald 1, P Andrew Futreal 7, Padmanee Sharma 10, James P Allison 10, Bertrand Routy 4 5 6, Laurence Zitvogel 26 27 28, Jennifer A Wargo 29 30;
1 Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
2 Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia.
3 Deparment of Medicine, Monash University, Melbourne, Victoria, Australia.
4 Gustave Roussy Cancer Campus (GRCC), Villejuif, France.
5 Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France.
6 Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France.
7 Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
8 Department of Dermatology, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
9 Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
10 Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
11 Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
12 MD Anderson Cancer Center University of Texas Health Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA.
13 AstraZeneca, Gaithersburg, MD, USA.
14 Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA.
15 Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
16 Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
17 Division of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
18 Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
19 Istituto Europeo di Oncologia, Milan, Italy.
20 Aix-Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France.
21 Department of Medicine, Faculty of Medicine and Health Sciences, McGill University Health Centre, Montreal, Quebec, Canada.
22 Cedars Cancer Center, McGill University Health Centre, Montreal, Quebec, Canada.
23 Division of Medical Oncology, University of Toronto, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada.
24 Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
25 Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
26 Gustave Roussy Cancer Campus (GRCC), Villejuif, France. laurence.zitvogel@gustaveroussy.fr.
27 Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France. laurence.zitvogel@gustaveroussy.fr.
28 Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France. laurence.zitvogel@gustaveroussy.fr.
29 Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. jwargo@mdanderson.org.
30 Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. jwargo@mdanderson.org.
# Contributed equally.
Identification of neoantigen-reactive T lymphocytes in the peripheral blood of a patient with glioblastoma
Leko V, et al.
Journal for ImmunoTherapy of Cancer
July 2021
Authors and Affiliates
Vid Leko 1, Gal Cafri 2, Rami Yossef 3, Biman Paria 4, Victoria Hill 3, Devikala Gurusamy 3, Zhili Zheng 3, Jared J Gartner 3, Todd D Prickett 3, Stephanie L Goff 3, Paul Robbins 3, Yong-Chen Lu 3, Steven A Rosenberg 3;
1 Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA vid.leko@nih.gov.
2 Sheba Medical Center, Ramat Gan, Israel.
3 Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA.
4 Program Coordination and Referral Branch, National Cancer Institute, Bethesda, Maryland, USA.
Clinical and basic implications of dynamic T cell receptor clonotyping in hematopoietic cell transplantation
Pagliuca S, et al.
JCI Insight
July 2021
Authors and Affiliates
Simona Pagliuca 1,2, Carmelo Gurnari 1,3, Sanghee Hong 4, Ran Zhao 5, Sunisa Kongkiatkamon 1, Laila Terkawi 1, Misam Zawit 1, Yihong Guan 1, Hassan Awada 1, Ashwin Kishtagari 1, Cassandra M Kerr 1, Thomas LaFramboise 6, Bhumika J Patel 7, Babal K Jha 1, Hetty E Carraway 4, Valeria Visconte 1, Navneet S Majhail 4, Betty K Hamilton 4, Jaroslaw P Maciejewski 1;
1 Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA.
2 University of Paris, Paris, France.
3 Department of Biomedicine and Prevention, School of Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
4 Blood and Marrow Transplant Program, Department of Hematology and Oncology and.
5 Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA.
6 Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
7 Leukemia and Myeloid Disorders Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA.
Deep learning identifies antigenic determinants of severe SARS-CoV-2 infection within T-cell repertoires
Sidhom JW and Baras AS
Scientific Reports
July 2021
Authors and Affiliates
John-William Sidhom 1,2,3, Alexander S Baras 4,5,6;
1 Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu.
2 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu.
3 Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu.
4 Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
5 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
6 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Evaluating T-cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance
Cottrell T, et al.
July 2021
Authors and Affiliates
Tricia Cottrell #,1,2,3, Jiajia Zhang #,2,4,5, Boyang Zhang 6, Genevieve J Kaunitz 7, Poromendro Burman 2,4,5, Hok-Yee Chan 2,4,5, Franco Verde 8, Jody E Hooper 1, Hans Hammers 4,9, Mohamad E Allaf 2,4, Hongkai Ji 6, Janis Taube 1,2,4,10, Kellie N Smith 11,4,5,10;
1 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
2 Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, USA.
3 Queen's Cancer Research Institute at Queens University, Kingston, Ontario, Canada.
4 Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA.
5 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
6 Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA.
7 Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
8 Department of Radiology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
9 Harold C. Simmons Comprehensive Cancer Center, Dallas, TX, USA.
10 The Mark Foundation Center for Advanced Genomics and Imaging, Baltimore, MD, USA.
11 Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, USA ksmit228@jhmi.edu.
# Contributed equally.
Humans with inherited T cell CD28 deficiency are susceptible to skin papillomaviruses but are otherwise healthy
Béziat V, et al.
Cell
July 2021
Authors and Affiliates
Vivien Béziat 1, Franck Rapaport 2, Jiafen Hu 3, Matthias Titeux 4, Mathilde Bonnet des Claustres 4, Mathieu Bourgey 5, Heather Griffin 6, Élise Bandet 4, Cindy S Ma 7, Roya Sherkat 8, Hassan Rokni-Zadeh 9, David M Louis 10, Majid Changi-Ashtiani 11, Ottavia M Delmonte 12, Toshiaki Fukushima 13, Tanwir Habib 14, Andrea Guennoun 14, Taushif Khan 14, Noemi Bender 15, Mahbuba Rahman 14, Frédégonde About 4, Rui Yang 2, Geetha Rao 7, Claire Rouzaud 16, Jingwei Li 3, Debra Shearer 3, Karla Balogh 3, Fatima Al Ali 14, Manar Ata 14, Soroosh Dabiri 17, Mana Momenilandi 18, Justine Nammour 4, Marie-Alexandra Alyanakian 19, Marianne Leruez-Ville 19, David Guenat 20, Marie Materna 4, Léa Marcot 4, Natasha Vladikine 4, Christine Soret 20, Hassan Vahidnezhad 21, Leila Youssefian 21, Amir Hossein Saeidian 21, Jouni Uitto 21, Émilie Catherinot 22, Shadi Sadat Navabi 23, Mohammed Zarhrate 4, David T Woodley 24, Mohamed Jeljeli 25, Thomas Abraham 3, Serkan Belkaya 2, Lazaro Lorenzo 4, Jérémie Rosain 16, Mousa Bayat 17, Fanny Lanternier 16, Olivier Lortholary 16, Faramarz Zakavi 26, Philippe Gros 27, Gérard Orth 28, Laurent Abel 29, Jean-Luc Prétet 20, Sylvie Fraitag 19, Emmanuelle Jouanguy 29, Mark M Davis 30, Stuart G Tangye 7, Luigi D Notarangelo 12, Nico Marr 14, Tim Waterboer 15, David Langlais 27, John Doorbar 6, Alain Hovnanian 16, Neil Christensen 3, Xavier Bossuyt 18, Mohammad Shahrooei 31, Jean-Laurent Casanova 32;
1 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA. Electronic address: vivien.beziat@inserm.fr.
2 The Rockefeller University, New York, NY 10065, USA.
3 Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
4 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France.
5 McGill University, Montreal, QC H3A 0G1, Canada.
6 University of Cambridge, Cambridge CB2 1QP, UK.
7 Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia.
8 Isfahan University of Medical Sciences, AIRC, Isfahan 81746-73461, Iran.
9 Zanjan University of Medical Sciences, Zanjan 45139-56184, Iran.
10 Stanford University Medical School, Stanford, CA 94305, USA.
11 Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran.
12 National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
13 Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
14 Sidra Medicine, Doha, Qatar.
15 German Cancer Research Center, 69120 Heidelberg, Germany.
16 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; Necker Hospital for Sick Children, AP-HP, 75015 Paris, France.
17 Zahedan University of Medical Sciences, 054 Zahedan, Iran.
18 University of Leuven, 3000 Leuven, Belgium.
19 Necker Hospital for Sick Children, AP-HP, 75015 Paris, France.
20 Papillomavirus National Reference Center, Besançon Hospital, 25030 Besançon, France.
21 Thomas Jefferson University, Philadelphia, PA 19107, USA.
22 Foch Hospital, 92150 Suresnes, France.
23 Dr. Shahrooei Lab, Ahvaz, Iran.
24 University of Southern California, Los Angeles, CA 90033, USA.
25 Cochin University Hospital, AP-HP, 75014 Paris, France.
26 Ahvaz Jundishapur University of Medical Sciences, 061 Ahvaz, Iran.
27 McGill University, Montreal, QC H3A 0G1, Canada; McGill Research Centre on Complex Traits, Montreal, QC H3G 0B1, Canada.
28 Pasteur Institute, 75015 Paris, France.
29 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA.
30 HHMI, Stanford University Medical School, Stanford, CA 94305, USA.
31 University of Leuven, 3000 Leuven, Belgium; Dr. Shahrooei Lab, Ahvaz, Iran.
32 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA; HHMI, New York, NY 10065, USA. Electronic address: casanova@rockefeller.edu.